[BioC] chromosome position --> gene

Sean Davis sdavis2 at mail.nih.gov
Mon Jun 27 01:11:42 CEST 2005


I don't think there is a direct function for doing this, but I could be 
wrong (and would love to be corrected).  However, I can think of at least 
three options:

1)  Output your chromosomes and locations in a format that can be used in 
the UCSC genome browser to construct a custom track, which is actually quite 
simple.  Then, you can "intersect" your custom track with other things 
available from the genome browser including, but not limited to, genes.

2)  You can download the table from the UCSC genome browser that you are 
interested in (or get it via the table browser).  Then, you can use that 
table to construct your own function.

3)  You could use RMySQL to directly query the EnsEMBL database to get the 
information you want.  This would require a bit of understanding of the 
EnsEMBL database and of SQL queries.  (See the biomaRt package for some 

Number 1 has two advantages:  you can intersect with with multiple 
annotations and it is probably less work.  Number 2 has the advantage that 
it can be done entirely from R (including the download).  If you are EnsEMBL 
centric and comfortable with SQL, number 3 may do it for you.


----- Original Message ----- 
From: "Sorani, Marco" <soranim at pharmacy.ucsf.edu>
To: <bioconductor at stat.math.ethz.ch>
Sent: Sunday, June 26, 2005 1:19 PM
Subject: [BioC] chromosome position --> gene

> Is there R code available that maps a chromosomal position (e.g., "chr2", 
> "80,000,000") or range (e.g., "chr2", "80,000,000 - 90,000,000") to a 
> gene?
> ******************
> soranim at pharmacy.ucsf.edu
> Marco Sorani
> Program in Biological & Medical Informatics
> University of California, San Francisco
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

More information about the Bioconductor mailing list